Presentation Information
[P04-573]Metagenomics and Single-Cell Genomics Reveal Microbial Functional Diversity in Suruga Bay as a Foundation for Marine Biotechnology
○Katsuhiko Mineta1,2,3, Yuu Abe1, Tatsumi Hasebe1, Renya Kobayashi1, Yuto Hiraki1, Takashi Yoshikawa4, Kenji Nohara4, Hiroshi Saito4, Yoshimoto Saito3, Takashi Gojobori3,5, Yohei Nishikawa1,6, Masahito Hosokawa1, Haruko Takeyama1 (1. Waseda University (Japan), 2. Shizuoka Institute of Science and Technology (Japan), 3. Marine Open Innovation (MaOI) Institute (Japan), 4. Tokai University (Japan), 5. National Cheng Kung University (Taiwan), 6. National Institute of Advanced Industrial Science and Technology (Japan))
Keywords:
Metagenomics,Single-cell genomics,Marine bioprospecting,Deep-sea microbiology,Marine bioresources
[Purpose]
Suruga Bay, located in central Japan, spans a depth gradient from coastal surface waters to depths exceeding 2,000 m. Its pronounced seasonal variability and anthropogenic influences make it an attractive natural laboratory for studying marine microbial ecosystems. From a marine biotechnology perspective, vertically stratified environments are expected to harbor microorganisms with distinct metabolic capacities and adaptive traits, representing valuable genetic resources. This study aims to establish a genomic baseline of microbial diversity and functional potential in Suruga Bay and to assess its significance as a reservoir of novel genes and metabolic pathways relevant to marine biotechnology.
[Method]
Since 2020, we have conducted systematic sampling at multiple stations and seasons in Suruga Bay under the BISHOP (Blue Innovation of Shizuoka Open Data Platform) initiative. Seawater samples were collected across depths and seasons to capture spatial and temporal variability. Shotgun metagenomic sequencing characterized taxonomic composition and functional gene repertoires. In parallel, single-cell genomics was used to obtain genome sequences, enabling high-resolution reconstruction of genomes to reveal metabolic potential often obscured in the metagenome datasets. Bioinformatics analyses included assembly, genome binning, quality assessment, functional annotation, and comparative analyses to identify depth-associated microbial and functional signatures.
[Results]
Metagenomic analyses revealed seasonal and depth-associated shifts in microbial community composition. Functional profiling demonstrated stratification of metabolic pathways across environmental gradients. Surface and deeper waters differed in the composition of genes associated with nutrient utilization, indicating functional differentiation along the depth gradient. Single-cell genomic analyses further resolved metabolic specialization at higher taxonomic resolution, uncovering lineage-specific gene repertoires among previously uncultured microorganisms. Together, these findings indicate structured functional diversity within microbial communities across the bay.
[Consideration]
The observed functional divergence suggests that Suruga Bay hosts vertically structured reservoirs of metabolic innovation. Microbial communities in different depth layers possess distinct genetic traits potentially relevant to marine biotechnology, including diverse capacities for nutrient transformation and environmental adaptation. Although targeted bioprospecting has not yet been conducted, the genomic features identified here suggest that Suruga Bay may serve as a promising resource for future bioprospecting aimed at discovering novel genes and biocatalytic functions. Integrating metagenomics with single-cell genomics improves access to high-quality genomic information from uncultured microorganisms, supporting data-driven discovery and sustainable utilization aligned with future blue economy initiatives.
[Conclusion]
Our integrated analyses provide a comprehensive genomic baseline of microbial functional diversity in Suruga Bay. The stratification of metabolic potential across environmental gradients highlights the bay as a promising reservoir of genes and adaptive traits relevant to marine biotechnology, laying the groundwork for future bioprospecting and responsible use of marine microbial bioresources.
Suruga Bay, located in central Japan, spans a depth gradient from coastal surface waters to depths exceeding 2,000 m. Its pronounced seasonal variability and anthropogenic influences make it an attractive natural laboratory for studying marine microbial ecosystems. From a marine biotechnology perspective, vertically stratified environments are expected to harbor microorganisms with distinct metabolic capacities and adaptive traits, representing valuable genetic resources. This study aims to establish a genomic baseline of microbial diversity and functional potential in Suruga Bay and to assess its significance as a reservoir of novel genes and metabolic pathways relevant to marine biotechnology.
[Method]
Since 2020, we have conducted systematic sampling at multiple stations and seasons in Suruga Bay under the BISHOP (Blue Innovation of Shizuoka Open Data Platform) initiative. Seawater samples were collected across depths and seasons to capture spatial and temporal variability. Shotgun metagenomic sequencing characterized taxonomic composition and functional gene repertoires. In parallel, single-cell genomics was used to obtain genome sequences, enabling high-resolution reconstruction of genomes to reveal metabolic potential often obscured in the metagenome datasets. Bioinformatics analyses included assembly, genome binning, quality assessment, functional annotation, and comparative analyses to identify depth-associated microbial and functional signatures.
[Results]
Metagenomic analyses revealed seasonal and depth-associated shifts in microbial community composition. Functional profiling demonstrated stratification of metabolic pathways across environmental gradients. Surface and deeper waters differed in the composition of genes associated with nutrient utilization, indicating functional differentiation along the depth gradient. Single-cell genomic analyses further resolved metabolic specialization at higher taxonomic resolution, uncovering lineage-specific gene repertoires among previously uncultured microorganisms. Together, these findings indicate structured functional diversity within microbial communities across the bay.
[Consideration]
The observed functional divergence suggests that Suruga Bay hosts vertically structured reservoirs of metabolic innovation. Microbial communities in different depth layers possess distinct genetic traits potentially relevant to marine biotechnology, including diverse capacities for nutrient transformation and environmental adaptation. Although targeted bioprospecting has not yet been conducted, the genomic features identified here suggest that Suruga Bay may serve as a promising resource for future bioprospecting aimed at discovering novel genes and biocatalytic functions. Integrating metagenomics with single-cell genomics improves access to high-quality genomic information from uncultured microorganisms, supporting data-driven discovery and sustainable utilization aligned with future blue economy initiatives.
[Conclusion]
Our integrated analyses provide a comprehensive genomic baseline of microbial functional diversity in Suruga Bay. The stratification of metabolic potential across environmental gradients highlights the bay as a promising reservoir of genes and adaptive traits relevant to marine biotechnology, laying the groundwork for future bioprospecting and responsible use of marine microbial bioresources.
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